From 56cf1072fad8f92f17ef1b997e3af549f664621e Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 20 Mar 2018 10:53:55 +0100
Subject: [PATCH] self reactions are layouted properly
---
.../sbml/reaction/SBOTermReactionType.java | 2 +-
.../small/reaction/self_reaction.xml | 57 +++++++++++++++++++
.../layout/ApplySimpleLayoutModelCommand.java | 9 ++-
3 files changed, 65 insertions(+), 3 deletions(-)
create mode 100644 converter-sbml/testFiles/small/reaction/self_reaction.xml
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java
index 5424c1e616..aa0f9c7eba 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java
@@ -60,7 +60,7 @@ public enum SBOTermReactionType {
}
}
if (result == null) {
- logger.warn("Don't know how to handle SBOTerm " + sboTerm + " for modifier");
+ logger.warn("Don't know how to handle SBOTerm " + sboTerm + " for reaction");
result = StateTransitionReaction.class;
}
return result;
diff --git a/converter-sbml/testFiles/small/reaction/self_reaction.xml b/converter-sbml/testFiles/small/reaction/self_reaction.xml
new file mode 100644
index 0000000000..eb9932349c
--- /dev/null
+++ b/converter-sbml/testFiles/small/reaction/self_reaction.xml
@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+ <model id="TestGEN">
+ <annotation/>
+ <listOfCompartments>
+ <compartment constant="true" id="default" name="cell" sboTerm="SBO:0000290" size="1">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+ <rdf:Description rdf:about="#">
+ <bqbiol:isVersionOf>
+ <rdf:Bag>
+ <rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
+ </rdf:Bag>
+ </bqbiol:isVersionOf>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </compartment>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="default" initialConcentration="1" id="s1588" name="NGFR" sboTerm="SBO:0000252">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+ <rdf:Description rdf:about="#">
+ <bqbiol:isEncodedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="urn:miriam:hgnc.symbol:NGFR"/>
+ </rdf:Bag>
+ </bqbiol:isEncodedBy>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </species>
+ </listOfSpecies>
+ <listOfReactions>
+<reaction reversible="false" id="r2149" sboTerm="SBO:0000170">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+ <rdf:Description rdf:about="#">
+ <bqbiol:isDescribedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="urn:miriam:pubmed:22236693 "/>
+ </rdf:Bag>
+ </bqbiol:isDescribedBy>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="s1588" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="s1588" stoichiometry="1"/>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
index fa528d3bf2..3a426da477 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
@@ -120,10 +120,10 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
Set<Species> elementToAlign = new HashSet<>();
Map<Compartment, Set<Element>> elementsByStaticCompartment = new HashMap<>();
for (Element element : elements) {
- if (element.getWidth()==0) {
+ if (element.getWidth() == 0) {
element.setWidth(SPECIES_WIDTH);
element.setHeight(SPECIES_HEIGHT);
-
+
}
if (element.getCompartment() == null || element.getCompartment() == parent) {
if (element instanceof Compartment) {
@@ -218,6 +218,11 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
Point2D middle = getMiddlePoint(productElement.getCenter(), reactantElement.getCenter());
+ //for self reactions
+ if (productElement.equals(reactantElement)) {
+ middle.setLocation(middle.getX(), middle.getY() + 50);
+ }
+
modifyProducts(reaction, middle);
modifyReactants(reaction, middle);
modifyModifiers(reaction, middle);
--
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